Results 181 to 190 of about 17,767 (219)

ASTER: A Package for Large-Scale Phylogenomic Reconstructions. [PDF]

Mol Biol Evol
Zhang C, Nielsen R, Mirarab S.
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Phylotranscriptomic analyses reveal deep gene tree discordance in Camellia (Theaceae)

Molecular Phylogenetics and Evolution, 2023
Gene tree discordance is a significant legacy of biological evolution. Multiple factors can result in incongruence among genes, such as introgression, incomplete lineage sorting (ILS), gene duplication or loss. Resolving the background of gene tree discordance is a critical way to uncover the process of species diversification.
Qiong Zhang, Ryan A. Folk, Zhi-Qiong Mo, Hang Ye, Zhao-Yuan Zhang, Hua Peng, Jian-Li Zhao, Shi-Xiong Yang, Xiang-Qin Yu   +8 more
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Coalescent histories for discordant gene trees and species trees

Theoretical Population Biology, 2010
Given a gene tree and a species tree, a coalescent history is a list of the branches of the species tree on which coalescences in the gene tree take place. Each pair consisting of a gene tree topology and a species tree topology has some number of possible coalescent histories.
Noah A, Rosenberg, James H, Degnan
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EXACT SOLUTIONS FOR SPECIES TREE INFERENCE FROM DISCORDANT GENE TREES

Journal of Bioinformatics and Computational Biology, 2013
Phylogenetic analysis has to overcome the grant challenge of inferring accurate species trees from evolutionary histories of gene families (gene trees) that are discordant with the species tree along whose branches they have evolved. Two well studied approaches to cope with this challenge are to solve either biologically informed gene tree parsimony ...
Wen-Chieh, Chang, Paweł, Górecki, Oliver, Eulenstein   +2 more
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Resolving Marine–Freshwater Transitions by Diatoms Through a Fog of Gene Tree Discordance

Systematic Biology, 2023
Abstract Despite the obstacles facing marine colonists, most lineages of aquatic organisms have colonized and diversified in freshwaters repeatedly. These transitions can trigger rapid morphological or physiological change and, on longer timescales, lead to increased rates of speciation and extinction.
Wade R Roberts, Elizabeth C Ruck, Kala M Downey, Eveline Pinseel, Andrew J Alverson   +4 more
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Gene tree discordance, phylogenetic inference and the multispecies coalescent

Trends in Ecology & Evolution, 2009
The field of phylogenetics is entering a new era in which trees of historical relationships between species are increasingly inferred from multilocus and genomic data. A major challenge for incorporating such large amounts of data into inference of species trees is that conflicting genealogical histories often exist in different genes throughout the ...
James H, Degnan, Noah A, Rosenberg
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Probabilistic Analysis Indicates Discordant Gene Trees in Chloroplast Evolution

Journal of Molecular Evolution, 2003
Analyses of whole-genome data often reveal that some genes have evolutionary histories that diverge from the majority phylogeny estimated for the entire genome. We present a probabilistic model that deals with heterogeneity among gene trees, implement it via the Gibbs sampler, and apply it to the plastid genome.
Claus, Vogl, Jonathan, Badger, Paul, Kearney, Ming, Li, Michael, Clegg, Tao, Jiang   +5 more
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Genomic data resolve gene tree discordance in spiderhunters (Nectariniidae, Arachnothera)

Molecular Phylogenetics and Evolution, 2018
Reduced representation genomic sequencing methods efficiently gather sequence data from thousands of loci throughout the genome. These data can be used to test previous phylogenetic hypotheses produced from limited numbers of mitochondrial and nuclear loci that often reveal intriguing, but conflicting, results.
Luke C, Campillo, Carl H, Oliveros, Frederick H, Sheldon, Robert G, Moyle   +3 more
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Phylogenomics of the Aphididae: Deep relationships between subfamilies clouded by gene tree discordance, introgression and the gene tree anomaly zone

Systematic Entomology, 2022
Abstract Aphids (Hemiptera: Aphididae) are a lineage of ~5200 plant‐feeding insects most abundant in temperate regions. The diversification of aphids is thought to be a rapid radiation, whereas abiotic and biotic factors heavily influence the morphologies.
Christopher L. Owen, Gary L. Miller
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Whole Genomes Reveal Evolutionary Relationships and Mechanisms Underlying Gene-Tree Discordance in Neodiprion Sawflies

Systematic Biology, 2023
Abstract Rapidly evolving taxa are excellent models for understanding the mechanisms that give rise to biodiversity. However, developing an accurate historical framework for comparative analysis of such lineages remains a challenge due to ubiquitous incomplete lineage sorting (ILS) and introgression. Here, we use a whole-genome alignment,
Danielle K Herrig, Ryan D Ridenbaugh, Kim L Vertacnik, Kathryn M Everson, Sheina B Sim, Scott M Geib, David W Weisrock, Catherine R Linnen   +7 more
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